This folder contains the data and code to reproduce the data and figures of the yeast perturbation networks. 

### Data

Inside the data folder we have:
- `processed_data`: all intermediate files that are needed for the analysis. The main one is `GSE125162_all_pseudobulk_logcounts.txt` that contains the pseudo-bulked data from the Inferelator paper. This is the starting point of all subsequent analysis
- `networks`: all networks and references to networks. To avoid storing too much data, we have here the references to the entire network data on AWS. 

### Code

In `src` we have the notebooks to reproduce all the analyses in the paper. 
- `bonobo_compute.ipynb`: compute bonobo networks
- `bonobo_compute_other_networks.ipynb`: compute lioness, spcc, sweet networks
- `bonobo_sparse_inferelator_gcn4.ipynb`: figures about the GCN4 edges
- `clustering_performance.ipynb`: clustering/distance performance of a single method
- `comparison_clustering_performance.ipynb`: comparisons between methods

### Results 

Results that come out of the notebooks (all but the compute networks steps).